Many theoretical issues were raised by our newer findings on the spectral and thermodynamic characterization of cytochrome aa3. Our finding that CO did not raise the Em of cytochrome a3 is contrary to theory for a case where a ligand binds more strongly to the reduced member of a redox couple. We proposed that protons are second ligands that bind more strongly to the oxidized member of the CO-liganded couple. A theoretical paper published early this year using other considerations reached the opposite conclusion. In an intensive theoretical examination of cooperativity for a system involving three ligands (electron, proton, and CO), we were able to explain how the later results do not rule out cooperative interactions involving protons and how multi-ligand interactions could be effectively utilized for a redox-drive Bohr-type proton pump. Other of our newer findings posed additional theoretical questions. We concluded that the redox potential of cytochrome a3 was under the control of the redox state of other centers in the molecule. We found that lowering the voltage first oxidized cytochrome a3 and then reduced it. Existing theory does not account for these phenomena. Cytochrome oxidase can theoretically possess from 4 to 13 redox centers. The Em of any center may be cooperatively affected by any combination of electrons in the other centers. We have started a quantitative theoretical consideration of the expected effects of redox interactions in a variety of possible models based on cytochrome oxidase. Preliminary results indicate that redox cooperativity can account for our newer results. A research collaboration was initiated with the laboratory of Britton Chance. Our newer intensive analytical techniques, in equilibrium studies, revealed specific spectral components and interactions. We hope to use the same analytical technique in kinetic studies coupled with our newer characterizations of the components to study the mechanism of cytochrome oxidase activity. Preliminary results do show the same kinds of spectra we had encountered in our work.